Download Database Modeling in Bioinformatics

The Proteome Analysis Database
http://www.ebi.ac.uk/proteome/
EMBL Outstation — The European Bioinformatics Institute
The Proteome Analysis Database - aims at integrating information
from a variety of sources that will together facilitate the classification
of the proteins in complete proteome sets.
Structural information includes amino acid composition
for each of the proteomes
and links are provided to
HSSP, the Homology derived Secondary Structure of Proteins, and
PDB, the Protein Data Bank, for individual proteins from
each of the proteomes.
Functional classification using Gene Ontology (GO) is available.
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
Complete proteome sets for each organism have been
assembled from
SPTR (SWISS-PROT + TrEMBL + TrEMBLnew) database
to be wholly non-redundant at the sequence level.
Archaeal, bacterial and the A. thaliana and S. cerevisiae proteome sets:
A standard procedure based on tracking protein identifiers from
the nucleotide sequence database EMBL-Bank is used.
D. melanogaster, C. elegans and H. sapiens proteome sets:
There are no unique identifiers in EMBL-Bank that allow the
identification of all genome-project sequences for these organisms.
Each of these organisms is treated separately as a special case.
EMBL Outstation — The European Bioinformatics Institute
Proteome sets
Where an organism contains more than 1 genomic component (chromosomes,
organelles, plasmids etc.), the set of proteins encoded by each are combined, and
any redundant members are removed from the composite set.
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
For D. melanogaster proteins, the complete set of are those
predicted from the Celera genomic sequence.
Each entry is tagged on entry into TrEMBL.
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
CHROMOSOME TABLES
Map proteins to chromosomes for yeast and human.
The information needed to make protein-chromosome mappings
is distributed over several databases.
Resources are pooled to make mappings.
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
30 biggest clusters
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute
Gene OntologyTM Consortium
produces a dynamic controlled
vocabulary that can be applied
to all eukaryotes.
EMBL Outstation — The European Bioinformatics Institute
The Proteome Analysis Database
Currently integrates data on 44 complete proteomes:
eukaryotes: 5 organisms
archaea:
8 organisms
bacteria: 31 organisms
EMBL Outstation — The European Bioinformatics Institute
InterPro: covers 31% to 67% of the proteins
from each of the complete genomes.
Eukaryote
Arabidopsis thaliana
65.5%
Drosophila melanogaster 67.8%
Caenorhabditis elegans
64.0%
Saccharomyces cerevisiae 61.7%
Homo sapiens 71.8% of the incomplete proteome (SWISS-PROT and TrEMBL)
59.7% of the complete proteome (SWISS-PROT, TrEMBL and Ensembl)
Bacteria
For example:
Bacillus subtilis
61.9%
Mycobacterium tuberculosis 64.7%
Xylella fastidiosa
47.5%
Rickettsia prowazekii 73.5%
Archaea
Halobacterium sp. NRC-1 57.2%
Pyrococcus abyssi 66.2%
EMBL Outstation — The European Bioinformatics Institute
CluSTr: covers the four complete eukaryotic genomes
and the incomplete human genome data
EMBL Outstation — The European Bioinformatics Institute
Summary
The Proteome Analysis Database provides a broad view
of the proteome data classified according to
signatures describing particular sequence motifs and
sequence similarities and
affords the option of examining various specific details like
structure or
functional classification.
EMBL Outstation — The European Bioinformatics Institute
Publication:
Apweiler R., Biswas M., Fleischmann W., Kanapin A.,
Karavidopoulou Y., Kersey P., Kriventseva E.V., Mittard V.,
Mulder N., Phan I., Zdobnov E.
"Proteome Analysis Database: online application of
InterPro and CluSTr for the functional classification of
proteins in whole genomes."
Nucleic Acids Res. 29(1):44-48(2001)
EMBL Outstation — The European Bioinformatics Institute
The SWISS-PROT group at the EBI
EMBL Outstation — The European Bioinformatics Institute
EMBL Outstation — The European Bioinformatics Institute